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g_hydorder(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				     g_hydorder(1)

NAME
g_hydorder - computes tetrahedrality parameters around a given atom VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_hydorder -f traj.xtc -n index.ndx -s topol.tpr -o intf.xpm -or raw.out -Spect intfspect.out -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -d enum -bw real -sgang1 real -sgang2 real -tblock int -nlevel int DESCRIPTION
The tetrahedrality order parameters can be determined around an atom. Both angle an distance order parameters are calculated. See P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details. This application calculates the orderparameter in a 3d-mesh in the box, and with 2 phases in the box gives the user the option to define a 2D interface in time separating the faces by specifying parame- ters -sgang1 and -sgang2 (It is important to select these judiciously) FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input Index file -s topol.tpr Input Run input file: tpr tpb tpa -o intf.xpm Output, Mult. X PixMap compatible matrix file -or raw.out Output, Opt., Mult. Generic output file -Spect intfspect.out Output, Opt., Mult. Generic output file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files -d enum z Direction of the normal on the membrane: z, x or y -bw real 1 Binwidth of box mesh -sgang1 real 1 tetrahedral angle parameter in Phase 1 (bulk) -sgang2 real 1 tetrahedral angle parameter in Phase 2 (bulk) -tblock int 1 Number of frames in one time-block average -nlevel int 100 Number of Height levels in 2D - XPixMaps SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_hydorder(1)

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g_disre(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_disre(1)

NAME
g_disre - analyzes distance restraints VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_disre -s topol.tpr -f traj.xtc -ds drsum.xvg -da draver.xvg -dn drnum.xvg -dm drmax.xvg -dr restr.xvg -l disres.log -n viol.ndx -q viol.pdb -c clust.ndx -x matrix.xpm -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ntop int -maxdr real -nlevels int -[no]third DESCRIPTION
g_disre computes violations of distance restraints. If necessary, all protons can be added to a protein molecule using the g_protonate program. The program always computes the instantaneous violations rather than time-averaged, because this analysis is done from a trajectory file afterwards it does not make sense to use time averaging. However, the time averaged values per restraint are given in the log file. An index file may be used to select specific restraints for printing. When the optional -q flag is given a .pdb file coloured by the amount of average violations. When the -c option is given, an index file will be read containing the frames in your trajectory corresponding to the clusters (defined in another manner) that you want to analyze. For these clusters the program will compute average violations using the third power averaging algorithm and print them in the log file. FILES
-s topol.tpr Input Run input file: tpr tpb tpa -f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -ds drsum.xvg Output xvgr/xmgr file -da draver.xvg Output xvgr/xmgr file -dn drnum.xvg Output xvgr/xmgr file -dm drmax.xvg Output xvgr/xmgr file -dr restr.xvg Output xvgr/xmgr file -l disres.log Output Log file -n viol.ndx Input, Opt. Index file -q viol.pdb Output, Opt. Protein data bank file -c clust.ndx Input, Opt. Index file -x matrix.xpm Output, Opt. X PixMap compatible matrix file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -ntop int 0 Number of large violations that are stored in the log file every step -maxdr real 0 Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data. -nlevels int 20 Number of levels in the matrix output -[no]thirdyes Use inverse third power averaging or linear for matrix output SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_disre(1)
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